https://ecoliwiki.org/colipedia/api.php?action=feedcontributions&feedformat=atom&user=54.211.91.134EcoliWiki - User contributions [en]2026-11-03T10:41:20ZUser contributionsMediaWiki 1.43.11https://ecoliwiki.org/colipedia/index.php?title=PMID:11222603&diff=1491750PMID:112226032014-09-14T09:42:43Z<p>54.211.91.134: Fill PMID: Page!</p>
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'''Sat, B, Hazan, R, Fisher, T, Khaner, H, Glaser, G and Engelberg-Kulka, H''' (2001) Programmed cell death in Escherichia coli: some antibiotics can trigger mazEF lethality. ''J. Bacteriol.'' '''183''':2041-5<br />
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The discovery of toxin-antitoxin gene pairs (also called addiction modules) on extrachromosomal elements of Escherichia coli, and particularly the discovery of homologous modules on the bacterial chromosome, suggest that a potential for programmed cell death may be inherent in bacterial cultures. We have reported on the E. coli mazEF system, a regulatable addiction module located on the bacterial chromosome. MazF is a stable toxin and MazE is a labile antitoxin. Here we show that cell death mediated by the E. coli mazEF module can be triggered by several antibiotics (rifampicin, chloramphenicol, and spectinomycin) that are general inhibitors of transcription and/or translation. These antibiotics inhibit the continuous expression of the labile antitoxin MazE, and as a result, the stable toxin MazF causes cell death. Our results have implications for the possible mode(s) of action of this group of antibiotics.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11222603 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC95100 PMC95100]<br />
Online version:[http://dx.doi.org/10.1128/JB.183.6.2041-2045.2001 10.1128/JB.183.6.2041-2045.2001]<br />
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Anti-Bacterial Agents/pharmacology; Antitoxins/genetics; Antitoxins/metabolism; Apoptosis; Bacterial Proteins/genetics; Bacterial Proteins/metabolism; Bacterial Toxins/genetics; Bacterial Toxins/metabolism; Culture Media; Escherichia coli/drug effects; Escherichia coli/growth & development; Gene Expression Regulation, Bacterial; Protein Biosynthesis/drug effects; Transcription, Genetic/drug effects<br />
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<references/></div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:11222603&diff=1491749PMID:112226032014-09-14T09:42:42Z<p>54.211.91.134: New PMID: Page!</p>
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<div>PMID on Demand placeholder</div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:1990972&diff=1491707PMID:19909722014-08-11T19:54:01Z<p>54.211.91.134: Fill PMID: Page!</p>
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'''Silbert, CK, Humphries, DE, Palmer, ME and Silbert, JE''' (1991) Effects of sulfate deprivation on the production of chondroitin/dermatan sulfate by cultures of skin fibroblasts from normal and diabetic individuals. ''Arch. Biochem. Biophys.'' '''285''':137-41<br />
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Human skin fibroblast monolayer cultures from two normal men, three Type I diabetic men, and one Type I diabetic woman were incubated with [3H]glucosamine in the presence of diminished concentrations of sulfate. Although total synthesis of [3H]chondroitin/dermatan glycosaminoglycans varied somewhat between cell lines, glycosaminoglycan production was not affected within any line when sulfate levels were decreased from 0.3 mM to 0.06 mM to 0.01 mM to 0 added sulfate. Lowering of sulfate concentrations resulted in diminished sulfation of chondroitin/dermatan in a progressive manner, so that overall sulfation dropped to as low as 19% for one of the lines. Sulfation of chondroitin to form chondroitin 4-sulfate and chondroitin 6-sulfate was progressively and equally affected by decreasing the sulfate concentration in the culture medium. However, sulfation to form dermatan sulfate was preserved to a greater degree, so that the relative proportion of dermatan sulfate to chondroitin sulfate increased. Essentially all the nonsulfated residues were susceptible to chondroitin AC lyase, indicating that little epimerization of glucuronic acid residues to iduronic acid had occurred in the absence of sulfation. These results confirm the previously described dependency of glucuronic/iduronic epimerization on sulfation, and indicate that sulfation of the iduronic acid-containing disaccharide residues of dermatan can take place with sulfate concentrations lower than those needed for 6-sulfation and 4-sulfation of the glucuronic acid-containing disaccharide residues of chondroitin. There were considerable differences among the six fibroblast lines in susceptibility to low sulfate medium and in the proportion of chondroitin 6-sulfate, chondroitin 4-sulfate, and dermatan sulfate. However, there was no pattern of differences between normals and diabetics.<br />
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Aggrecans; Cells, Cultured; Chondroitin Lyases/pharmacology; Chondroitin Sulfate Proteoglycans/metabolism; Diabetes Mellitus/metabolism; Extracellular Matrix Proteins; Female; Fibroblasts/drug effects; Fibroblasts/metabolism; Glucuronates/metabolism; Glucuronic Acid; Glycoproteins/metabolism; Humans; Iduronic Acid/metabolism; Lectins, C-Type; Male; Proteoglycans; Tritium<br />
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<references/></div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:1990972&diff=1491706PMID:19909722014-08-11T19:54:00Z<p>54.211.91.134: New PMID: Page!</p>
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<div>PMID on Demand placeholder</div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:233425&diff=1491643PMID:2334252014-08-04T18:11:43Z<p>54.211.91.134: Fill PMID: Page!</p>
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'''Jacobitz, K, Achinger, R, Ostertag, H and Seitz, HD''' (1979) [Three different tumors in a case of synovial sarcoma of the hand]. ''Handchirurgie'' '''11''':239-41<br />
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Examining a 74 year old female patient with a nodular goiter, a tumor of the left thenar eminence with a concurrent radiolucent swelling in the adjoining second metacarpal was found. The diagnosis was a struma nodosa with regressive marginal changes, a hypervascularized monophasic synovial sarcoma of the wrist joint, and an enchondroma of the second metacarpal bone. Following the amputation of the forearm, no radiotherapy or cytotoxic therapy was performed. After a follow-up time of one year no metastases were detected.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=233425 PubMed]<br />
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Aged; Amputation; Chondroma/complications; Chondroma/surgery; Female; Hand/surgery; Humans; Metacarpus/surgery; Neoplasms, Multiple Primary/diagnosis; Neoplasms, Multiple Primary/surgery; Sarcoma, Synovial/complications; Sarcoma, Synovial/surgery; Thyroid Neoplasms/complications<br />
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<references/></div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:233425&diff=1491642PMID:2334252014-08-04T18:11:43Z<p>54.211.91.134: New PMID: Page!</p>
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<div>PMID on Demand placeholder</div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:8185318&diff=1491637PMID:81853182014-08-04T14:31:12Z<p>54.211.91.134: Fill PMID: Page!</p>
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'''Yoshimoto, T, Orawski, AT and Simmons, WH''' (1994) Substrate specificity of aminopeptidase P from Escherichia coli: comparison with membrane-bound forms from rat and bovine lung. ''Arch. Biochem. Biophys.'' '''311''':28-34<br />
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The substrate specificity of recombinant E. coli aminopeptidase P (aminoacylprolylpeptide hydrolase) (EC 3.4.11.9) was studied using about 150 synthetic peptides. E. coli aminopeptidase P released the N-terminal amino acid from most peptides containing a penultimate proline, although the relative rates of hydrolysis varied over two orders of magnitude. Dipeptides (X-Pro) were hydrolyzed relatively slowly. Detailed kinetic analysis using peptides of different lengths suggested that the enzyme has at least four subsites for interaction with substrates, namely S1, S'1, S'2, and S'3. S1 and S'1 have high stereo-specificity Various Pro-X dipeptides where X is a hydrophobic amino acid were competitive inhibitors of the enzyme. The substrate specificity of E. coli aminopeptidase P was compared to that of purified bovine lung and rat lung membrane-bound aminopeptidase P. The mammalian enzymes had much more restricted substrate specificities. The differences appeared to be due primarily to differences in the S'2 subsite. The E. coli enzyme could accommodate bulky amino acid side chains in the S'2 subsite, whereas the mammalian membrane-bound enzymes could not.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8185318 PubMed]<br />
Online version:[http://dx.doi.org/10.1006/abbi.1994.1204 10.1006/abbi.1994.1204]<br />
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Amino Acid Sequence; Aminopeptidases/chemistry; Aminopeptidases/metabolism; Animals; Cattle; Cell Membrane/enzymology; Escherichia coli/enzymology; Kinetics; Lung/enzymology; Molecular Sequence Data; Rats; Recombinant Proteins/metabolism; Substrate Specificity<br />
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<references/></div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:8185318&diff=1491636PMID:81853182014-08-04T14:31:12Z<p>54.211.91.134: New PMID: Page!</p>
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<div>PMID on Demand placeholder</div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:6991475&diff=1491633PMID:69914752014-08-04T14:20:54Z<p>54.211.91.134: Fill PMID: Page!</p>
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'''Staskawicz, BJ and Panopoulos, NJ''' (1980) Phaseolotoxin transport in Escherichia coli and Salmonella typhimurium via the oligopeptide permease. ''J. Bacteriol.'' '''142''':474-9<br />
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Phaseolotoxin [(N delta-phosphosulfamyl)ornithylalanylhomoarginine], a phytotoxic tripeptide produced by Pseudomonas syringae pv. phaseolicola that inhibits ornithine carbamoyltransferase, is transported into Escherichia coli and Salmonella typhimurium via the oligopeptide transport system (Opp). Mutants defective in oligopeptide permease (Opp-) were resistant to phaseolotoxin. Spontaneous phaseolotoxin-resistant mutants (Toxr) lacked the Opp function as evidenced by their cross-resistance to triornithine and failure to utilize glycylhistidylglycine as a source of histidine. Growth inhibition by phaseolotoxin was prevented by peptides known to be transported via the Opp system and by treatment of the toxin with L-aminopeptidase. In both E. coli and S. typhimurium, Toxr mutations were cotransducible with trp, suggesting that the opp locus occupies similar positions in genetic maps of these bacteria.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6991475 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC294006 PMC294006]<br />
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Bacterial Toxins/metabolism; Bacterial Toxins/pharmacology; Chromosome Mapping; Drug Resistance, Microbial; Escherichia coli/genetics; Escherichia coli/metabolism; Membrane Transport Proteins/metabolism; Mutation; Oligopeptides; Pseudomonas; Salmonella typhimurium/genetics; Salmonella typhimurium/metabolism<br />
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<references/></div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:6991475&diff=1491632PMID:69914752014-08-04T14:20:53Z<p>54.211.91.134: New PMID: Page!</p>
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<div>PMID on Demand placeholder</div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:2040681&diff=1491621PMID:20406812014-07-31T15:02:59Z<p>54.211.91.134: Fill PMID: Page!</p>
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'''Caranasos, GJ and Israel, R''' (1991) Gait disorders in the elderly. ''Hosp. Pract. (Off. Ed.)'' '''26''':67-70, 75, 79-82 passim<br />
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No abstract in PubMed<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2040681 PubMed]<br />
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Aged; Aged, 80 and over; Aging/physiology; Diagnosis, Differential; Dizziness/diagnosis; Dizziness/etiology; Dizziness/physiopathology; Dizziness/therapy; Gait/physiology; Humans; Male; Movement Disorders/diagnosis; Movement Disorders/etiology; Movement Disorders/physiopathology; Movement Disorders/therapy; Postural Balance/physiology<br />
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<references/></div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:2040681&diff=1491620PMID:20406812014-07-31T15:02:58Z<p>54.211.91.134: New PMID: Page!</p>
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'''Ho, YS and Rosenberg, M''' (1985) Characterization of a third, cII-dependent, coordinately activated promoter on phage lambda involved in lysogenic development. ''J. Biol. Chem.'' '''260''':11838-44<br />
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Lysogenic development by bacteriophage lambda is known to require the coordinate expression of two phage operons. Coordinate control is achieved by a positive regulatory mechanism which activates transcription from the promoters of these operons, PRE and PI. The positive effector is the phage regulatory protein cII. We now identify and characterize a third cII-dependent transcription unit on phage lambda, which is positioned in the middle of the Q regulatory gene and has an anti-Q orientation. We demonstrate the cII-dependent function of this promoter and precisely map its 5' transcription start-site both in vitro and in vivo. Most importantly, we show that cII binding and transcription activation at PaQ occur at essentially the same cII levels as those required for PRE and PI activation, and that all three promoters respond to cII at the same time following phage infection. In addition, DNase protection studies demonstrate that cII selectively interacts with the same TTGCN6TTGC DNA sequence repeat in the -35 region of PaQ which cII interacts with at both PRE and PI. We find that cII also binds other TTGCN6TTGC repeat sequences on lambda but binding at these sites does not lead to productive transcription. We conclude that PaQ functions in concert with PRE and PI to regulate the lysogenic growth response of phage lambda. We presume that the PaQ directed anti-sense Q RNA transcript functions to down-regulate the expression of the Q gene, which is needed for the expression of all phage late genes during lytic growth.<br />
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Bacteriophage lambda/genetics; DNA-Directed RNA Polymerases; Genes, Viral; Lysogeny; Promoter Regions, Genetic; Repetitive Sequences, Nucleic Acid; Sequence Homology, Nucleic Acid; Transcription, Genetic; Viral Proteins/pharmacology<br />
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{{LitSignificance}}<br />
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<references/></div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:2931430&diff=1491612PMID:29314302014-07-29T07:29:29Z<p>54.211.91.134: New PMID: Page!</p>
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<div>PMID on Demand placeholder</div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=Category:GO:0019073_!_viral_DNA_genome_packaging&diff=1491607Category:GO:0019073 ! viral DNA genome packaging2014-07-28T07:21:15Z<p>54.211.91.134: New GO term category page</p>
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<div>{{GO term stub|GO:0019073_!_viral_DNA_genome_packaging}}<br />
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==References==<br />
{{RefHelp}}<br />
<references/></div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:9520390&diff=1491527PMID:95203902014-07-22T07:30:53Z<p>54.211.91.134: Fill PMID: Page!</p>
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'''Wilce, MC, Bond, CS, Dixon, NE, Freeman, HC, Guss, JM, Lilley, PE and Wilce, JA''' (1998) Structure and mechanism of a proline-specific aminopeptidase from Escherichia coli. ''Proc. Natl. Acad. Sci. U.S.A.'' '''95''':3472-7<br />
|-<br />
!align=left |Abstract<br />
||<br />
The structure of the proline-specific aminopeptidase (EC 3.4.11.9) from Escherichia coli has been solved and refined for crystals of the native enzyme at a 2.0-A resolution, for a dipeptide-inhibited complex at 2.3-A resolution, and for a low-pH inactive form at 2.7-A resolution. The protein crystallizes as a tetramer, more correctly a dimer of dimers, at both high and low pH, consistent with observations from analytical ultracentrifuge studies that show that the protein is a tetramer under physiological conditions. The monomer folds into two domains. The active site, in the larger C-terminal domain, contains a dinuclear manganese center in which a bridging water molecule or hydroxide ion appears poised to act as the nucleophile in the attack on the scissile peptide bond of Xaa-Pro. The metal-binding residues are located in a single subunit, but the residues surrounding the active site are contributed by three subunits. The fold of the protein resembles that of creatine amidinohydrolase (creatinase, not a metalloenzyme). The C-terminal catalytic domain is also similar to the single-domain enzyme methionine aminopeptidase that has a dinuclear cobalt center.<br />
|-<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9520390 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC19860 PMC19860]<br />
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|-<br />
!align=left |Keywords<br />
||<br />
Aminopeptidases/chemistry; Aminopeptidases/genetics; Aminopeptidases/metabolism; Binding Sites; Escherichia coli/enzymology; Hydrogen-Ion Concentration; Molecular Sequence Data; Protein Conformation; Structure-Activity Relationship; Substrate Specificity<br />
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==Significance {{HelpIcon|Help:Literature}} ==<br />
{{LitSignificance}}<br />
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== Useful Materials and Methods {{HelpIcon|Help:Literature}}==<br />
{{LitMaterials}}<br />
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{{LitLinks}}<br />
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==See also==<br />
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==References==<br />
{{RefHelp}}<br />
<references/></div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:9520390&diff=1491526PMID:95203902014-07-22T07:30:52Z<p>54.211.91.134: New PMID: Page!</p>
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<div>PMID on Demand placeholder</div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:1211938&diff=1491508PMID:12119382014-07-21T05:05:08Z<p>54.211.91.134: Fill PMID: Page!</p>
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'''Chou, CC and Marth, EH''' (1975) Incorporation of (2-14C)acetate into lipids of mink (Mustela vison) liver and intestine during in vitro and in vivo treatment with aflatoxin B1. ''Appl Microbiol'' '''30''':946-50<br />
|-<br />
!align=left |Abstract<br />
||<br />
The in vitro and in vivo incorporation of (2-14C)acetate into lipids of mink (Mustela vison) liver and intestines was studied. In vitro, a dose of aflatoxin B1 as small as 7.5 mug/ml of medium reduced by 20% the amount of (2-14C)acetate incorporated into lipids of mink liver slices, whereas 180 mug caused 76% reduction in the synthesis of lipids from the radioactive precusor. Similar inhibition of lipid synthesis by aflatoxin also was observed with tissues from mink intestines and fatty liver. The degree of inhibition (19 to 84% for tissue from intestines and 19 to 64% for tissue from fatty livers) depended on the amount of aflatoxin B1 (7.5 TO 180 MUG) present in the medium. In vivo, a substantially increased amount of 14C-labeled lipids was found in the livers of mink injected with 600 mug of aflatoxin B1 per kg of body weight 20, 28, and 40 h earlier. However, no appreciable difference in incorporation of (2-14C)acetate into lipids was observed between toxin-treated and control animals when these animals were sacrificed and examined for 14C-labeled lipids at 4 and 10 h after toxin was administered.<br />
|-<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1211938 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC376573 PMC376573]<br />
<br />
|-<br />
!align=left |Keywords<br />
||<br />
Acetates/metabolism; Aflatoxins/pharmacology; Animals; Carbon Radioisotopes; Cholesterol/biosynthesis; Culture Techniques; Fatty Acids, Nonesterified/biosynthesis; Fatty Liver/metabolism; Female; Intestines/metabolism; Lipids/biosynthesis; Liver/metabolism; Mink; Phospholipids/biosynthesis; Triglycerides/biosynthesis<br />
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==Significance {{HelpIcon|Help:Literature}} ==<br />
{{LitSignificance}}<br />
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{{LitMaterials}}<br />
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<annotationlinks/><br />
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{{LitLinks}}<br />
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==References==<br />
{{RefHelp}}<br />
<references/></div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:1211938&diff=1491507PMID:12119382014-07-21T05:02:36Z<p>54.211.91.134: New PMID: Page!</p>
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<div>PMID on Demand placeholder</div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:230505&diff=1491470PMID:2305052014-07-13T06:35:42Z<p>54.211.91.134: Fill PMID: Page!</p>
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'''Gellert, M, Fisher, LM and O'Dea, MH''' (1979) DNA gyrase: purification and catalytic properties of a fragment of gyrase B protein. ''Proc. Natl. Acad. Sci. U.S.A.'' '''76''':6289-93<br />
|-<br />
!align=left |Abstract<br />
||<br />
A protein isolated from Escherichia coli complements the DNA gyrase A (NalA) protein to generate an activity that relaxes supercoiled DNA. Oxolinic acid, a known inhibitor of DNA gyrase, blocks this activity and causes double-strand cleavage of DNA at the same sites as are attacked by DNA gyrase. The protein, of molecular weight 50,000, appears to be fragment of the DNA gyrase B (Cou) protein (molecular weight, 90,000) as judged by the identical sizes of numerous peptides produced by partial proteolytic digestion. The complex of this fragment and the gyrase A protein lacks both the DNA-supercoiling and DNA-dependent ATPase activities of DNA gyrase.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=230505 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC411849 PMC411849]<br />
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|-<br />
!align=left |Keywords<br />
||<br />
Catalysis; DNA Topoisomerases, Type II/isolation & purification; DNA Topoisomerases, Type II/metabolism; DNA, Superhelical/pharmacology; Endonucleases/metabolism; Escherichia coli/enzymology; Macromolecular Substances; Molecular Weight; Oxolinic Acid/pharmacology; Topoisomerase II Inhibitors<br />
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{{LitSignificance}}<br />
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{{LitMaterials}}<br />
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{{LitLinks}}<br />
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<references/></div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:230505&diff=1491469PMID:2305052014-07-13T06:35:41Z<p>54.211.91.134: New PMID: Page!</p>
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<div>PMID on Demand placeholder</div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:2160049&diff=1491458PMID:21600492014-07-12T21:14:58Z<p>54.211.91.134: Fill PMID: Page!</p>
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||<br />
'''Miura-Masuda, A and Ikeda, H''' (1990) The DNA gyrase of Escherichia coli participates in the formation of a spontaneous deletion by recA-independent recombination in vivo. ''Mol. Gen. Genet.'' '''220''':345-52<br />
|-<br />
!align=left |Abstract<br />
||<br />
A system for detecting a spontaneous deletion in Escherichia coli was developed and the role of DNA gyrase in deletion formation was studied. A derivative of lambda plac5, lambda AM36, was isolated in which whole pBR322 DNA was inserted in the lacZ gene and 227 bp of the lac gene duplicated at both sides of the pBR322 DNA. E. coli lac- strains lysogenized by lambda AM36 had a Lac- phenotype and segregated Lac+ revertants. Sequence analyses showed that the revertant was formed by a deletion that eliminated the inserted pBR322 DNA and one copy of the duplicated segments. The frequency of lac+ revertant formation was independent of recA function, was increased by oxolinic acid, an inhibitor of DNA gyrase, but was not increased in a lysogen of a nalidixic acid-resistant derivative. The reversion frequencies of temperature sensitive mutants of gyrA gene are 10 to 100 times lower than that of the wild-type strain. These results indicate that the DNA gyrase of E. coli participated in the in vivo deletion formation resulting from the direct repeats.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2160049 PubMed]<br />
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|-<br />
!align=left |Keywords<br />
||<br />
Chromosome Deletion; Cloning, Molecular; DNA Topoisomerases, Type II/metabolism; DNA Transposable Elements; DNA, Bacterial/genetics; Escherichia coli/enzymology; Escherichia coli/genetics; Genes, Bacterial; Lac Operon; Mutation; Oxolinic Acid/pharmacology; Plasmids; Rec A Recombinases/genetics; Recombination, Genetic; Repetitive Sequences, Nucleic Acid; Temperature<br />
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{{LitSignificance}}<br />
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{{LitMaterials}}<br />
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{{LitLinks}}<br />
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==References==<br />
{{RefHelp}}<br />
<references/></div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:2160049&diff=1491457PMID:21600492014-07-12T21:14:57Z<p>54.211.91.134: New PMID: Page!</p>
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<div>PMID on Demand placeholder</div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:4897523&diff=1491448PMID:48975232014-07-12T07:20:21Z<p>54.211.91.134: Fill PMID: Page!</p>
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'''Chao, J, Johnson, GF and Graves, DJ''' (1969) Kinetic mechanism of maltodextrin phosphorylase. ''Biochemistry'' '''8''':1459-66<br />
|-<br />
!align=left |Abstract<br />
||<br />
No abstract in PubMed<br />
|-<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=4897523 PubMed]<br />
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|-<br />
!align=left |Keywords<br />
||<br />
Carbon Isotopes; Chemical Phenomena; Chemistry; Escherichia coli/enzymology; Glucose; Glucosyltransferases/antagonists & inhibitors; Hexosephosphates; Kinetics; Maltose; Phosphorus Isotopes; Polysaccharides; Spectrophotometry; Uracil Nucleotides<br />
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==Significance {{HelpIcon|Help:Literature}} ==<br />
{{LitSignificance}}<br />
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{{LitMaterials}}<br />
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{{LitLinks}}<br />
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==References==<br />
{{RefHelp}}<br />
<references/></div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:4897523&diff=1491447PMID:48975232014-07-12T07:20:20Z<p>54.211.91.134: New PMID: Page!</p>
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<div>PMID on Demand placeholder</div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:4146873&diff=1491407PMID:41468732014-07-03T21:49:42Z<p>54.211.91.134: Fill PMID: Page!</p>
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'''Raunio, RP, Straus, LD and Jenkins, WT''' (1973) D-alanine oxidase from Escherichia coli: participation in the oxidation of L-alanine. ''J. Bacteriol.'' '''115''':567-73<br />
|-<br />
!align=left |Abstract<br />
||<br />
Cell wall-membrane preparations of Escherichia coli, prepared by the ethylenediaminetetraacetic acid-lysozyme method, contain enzymes which catalyze the oxidation of d-alanine and, to a lesser extent, l-alanine into pyruvate and ammonia without the formation of hydrogen peroxide. The kinetic parameters were (i) pH optima of 8.3 to 8.4 for l- and d-alanine and (ii) a K(m) value of 6.6 +/- 0.2 mM for d-alanine. Several coenzymes were without effect when added to the reaction mixture. The participation of d-alanine oxidase in the oxidation of l-alanine was demonstrated. The evidence is based on (i) results of cellular fractionation; (ii) labeling experiments; (iii) inhibition studies with aminooxyacetate and cycloserine; (iv) denaturation experiments; and (v) demonstration of the presence of an active racemase.<br />
|-<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=4146873 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC246284 PMC246284]<br />
<br />
|-<br />
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||<br />
Acetates/pharmacology; Alanine/metabolism; Amino Acid Isomerases/antagonists & inhibitors; Amino Acid Isomerases/metabolism; Ammonia/biosynthesis; Cell Fractionation; Cell Membrane/enzymology; Cell-Free System; Cycloserine/pharmacology; D-Amino-Acid Oxidase/antagonists & inhibitors; D-Amino-Acid Oxidase/metabolism; Deoxycholic Acid/pharmacology; Edetic Acid; Escherichia coli/enzymology; Escherichia coli/metabolism; Hot Temperature; Hydrogen-Ion Concentration; Muramidase; Oxidation-Reduction; Oxygen Consumption; Pyruvates/biosynthesis; Stereoisomerism<br />
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{{LitSignificance}}<br />
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{{LitMaterials}}<br />
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<annotationlinks/><br />
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{{LitLinks}}<br />
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==References==<br />
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<references/></div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:4146873&diff=1491406PMID:41468732014-07-03T21:49:42Z<p>54.211.91.134: New PMID: Page!</p>
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<div>PMID on Demand placeholder</div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:126236&diff=1491365PMID:1262362014-07-01T07:44:06Z<p>54.211.91.134: Fill PMID: Page!</p>
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||<br />
'''Karu, AE, Sakaki, Y, Echols, H and Linn, S''' (1975) The gamma protein specified by bacteriophage gamma. Structure and inhibitory activity for the recBC enzyme of Escherichia coli. ''J. Biol. Chem.'' '''250''':7377-87<br />
|-<br />
!align=left |Abstract<br />
||<br />
The protein encoded by the gam gene of bacteriophage lambda ("gamma protein") is a specific inhibitor of the recBC enzyme of Escherichia coli. The lambda protein has been purified approximately 2,000-fold, and its structure and inhibitory activity have been characterized. It appears to be composed of two identical subunits of 16,500 daltons, inhibits all of the catalytic activities of the recBC enzyme with apparently equal efficiency, but has no effect upon any other E. coli or lambda-DNase tested. Inhibition does not occur unless recBC enzyme is exposed to gamma protein prior to reaction of the enzyme with DNA. The inhibitory activity is independent of temperature, and no catalytic activity has been detected that might fulfill the inhibitory function. It appears instead that the inhibition involves a stoichiometric, rather than a catalytic interaction between gamma protein and the enzyme. Reaction kinetics for the recBC enzyme inhibited by gamma protein show no anomalous protein--only a depressed rate. Inhibition is not competitive and does not appear to affect the enzyme's affinity for DNA. The enzyme remains inhibited after it is separated from "excess" gamma protein by gel filtration or sedimentation in a glycerol gradient, and inhibited enzyme has a reduced electrophoretic mobility compared to that of uninhibited enzyme. Gamma Protein inhibits recBC enzyme which has been reconstituted from cell-free extracts by complementation in vitro, but at least one of the complementing factors present in extracts from recB- cells does not by itself form a complex with gamma protein. The mechanism of inhibition and the implications of these results from gamma replication and recombination are discussed.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=126236 PubMed]<br />
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||<br />
Adenosine Triphosphatases/metabolism; Coliphages/analysis; Coliphages/metabolism; DNA; Endonucleases/metabolism; Escherichia coli/drug effects; Escherichia coli/metabolism; Exonucleases/metabolism; Genetic Code; Kinetics; Macromolecular Substances; Molecular Weight; Viral Proteins/isolation & purification; Viral Proteins/pharmacology<br />
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<references/></div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:126236&diff=1491364PMID:1262362014-07-01T07:44:05Z<p>54.211.91.134: New PMID: Page!</p>
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'''Popovic, A, Wu, B, Arrowsmith, CH, Edwards, AM, Davidson, AR and Maxwell, KL''' (2012) Structural and biochemical characterization of phage λ FI protein (gpFI) reveals a novel mechanism of DNA packaging chaperone activity. ''J. Biol. Chem.'' '''287''':32085-95<br />
|-<br />
!align=left |Abstract<br />
||<br />
One of the final steps in the morphogenetic pathway of phage λ is the packaging of a single genome into a preformed empty head structure. In addition to the terminase enzyme, the packaging chaperone, FI protein (gpFI), is required for efficient DNA packaging. In this study, we demonstrate an interaction between gpFI and the major head protein, gpE. Amino acid substitutions in gpFI that reduced the strength of this interaction also decreased the biological activity of gpFI, implying that this head binding activity is essential for the function of gpFI. We also show that gpFI is a two-domain protein, and the C-terminal domain is responsible for the head binding activity. Using nuclear magnetic resonance spectroscopy, we determined the three-dimensional structure of the C-terminal domain and characterized the helical nature of the N-terminal domain. Through structural comparisons, we were able to identify two previously unannotated prophage-encoded proteins with tertiary structures similar to gpFI, although they lack significant pairwise sequence identity. Sequence analysis of these diverse homologues led us to identify related proteins in a variety of myo- and siphophages, revealing that gpFI function has a more highly conserved role in phage morphogenesis than was previously appreciated. Finally, we present a novel model for the mechanism of gpFI chaperone activity in the DNA packaging reaction of phage λ.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=22801427 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3442539 PMC3442539]<br />
Online version:[http://dx.doi.org/10.1074/jbc.M112.378349 10.1074/jbc.M112.378349]<br />
|-<br />
!align=left |Keywords<br />
||<br />
Amino Acid Sequence; Bacteriophage lambda/chemistry; Bacteriophage lambda/enzymology; Catalysis; Chromatography, Gel; DNA Packaging; DNA, Viral/genetics; Endodeoxyribonucleases/chemistry; Genome, Viral; Magnetic Resonance Spectroscopy/methods; Molecular Sequence Data; Protein Binding/genetics; Protein Conformation; Protein Interaction Mapping; Protein Structure, Tertiary; Recombinant Proteins/chemistry; Sequence Homology, Amino Acid<br />
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<references/></div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:22801427&diff=1491362PMID:228014272014-07-01T06:37:29Z<p>54.211.91.134: New PMID: Page!</p>
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'''Daldal, F, Babul, J, Guixé, V and Fraenkel, DG''' (1982) An alteration in phosphofructokinase 2 of Escherichia coli which impairs gluconeogenic growth and improves growth on sugars. ''Eur. J. Biochem.'' '''126''':373-9<br />
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||<br />
Escherichia coli contains a major phosphofructokinase isoenzyme, phosphofructokinase 1, which is allosteric, and a minor isoenzyme, phosphofructokinase 2. The pfkB1 mutation is known to increase the amount of phosphofructokinase 2 and allow growth on sugars of mutants lacking phosphofructokinase 1; it does not affect growth on substances such as glycerol or lactate (i.e., 'gluconeogenic growth'). However, gluconeogenic growth is markedly impaired in strains with a different allele, pfkB1*. We show here that strains with pfkB1* contain an altered form of phosphofructokinase 2, called phosphofructokinase 2*, which has been purified. Phosphofructokinase 2* is cold labile and has slightly different kinetic characteristics from phosphofructokinase 2, which include being less sensitive to inhibition by fructose 1,6-bisphosphate. The Km for fructose 6-phosphate is low (about 5 X 10(-5) M) in both phosphofructokinase 2 and phosphofructokinase 2*. However, in strains lacking phosphofructokinase 1, a high level of phosphofructokinase 2 is associated with unusually high concentrations of hexose monophosphates during growth on glucose, while a strain with phosphofructokinase 2* instead of phosphofructokinase 2 grows more rapidly on glucose and contains lower levels of hexose monophosphates. In gluconeogenic conditions, by contrast, hexose monophosphate levels are normal in phosphofructokinase 2 strains, while the impaired growth of phosphofructokinase 2* strains is associated with high levels of fructose 2,6-bisphosphate and very low levels of hexose monophosphates. These results show that phosphofructokinase 2, as studied in vitro, should no longer be regarded as a 'non-allosteric' protein, a conclusion also reached by Kotlarz and Buc on the basis of different types of experiments [Eur. J. Biochem. 117, 569-574 (1981)]. The fact that mutational alteration of phosphofructokinase 2 allows more rapid growth on glucose but severely impairs gluconeogenic growth is an indication of the significance of the regulation in vivo. The more rapid growth of the mutant on glucose might be explained on the basis of decreased sensitivity to an inhibitor (possibly, but not necessarily, fructose 1,6-bisphosphate), although other models are possible. A variety of speculations are offered as to the mechanism of gluconeogenic impairment.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6215246 PubMed]<br />
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Carbohydrates/pharmacology; Electrophoresis, Polyacrylamide Gel; Escherichia coli/enzymology; Escherichia coli/genetics; Escherichia coli/growth & development; Gluconeogenesis; Isoenzymes/physiology; Phosphofructokinase-1/genetics; Phosphofructokinase-1/physiology<br />
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<references/></div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:6215246&diff=1491329PMID:62152462014-06-28T12:29:17Z<p>54.211.91.134: New PMID: Page!</p>
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<div>PMID on Demand placeholder</div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:2068975&diff=1491289PMID:20689752014-06-23T16:13:08Z<p>54.211.91.134: Fill PMID: Page!</p>
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'''Guengerich, FP, Shimada, T, Bondon, A and Macdonald, TL''' (1991) Cytochrome P-450 oxidations and the generation of biologically reactive intermediates. ''Adv. Exp. Med. Biol.'' '''283''':1-11<br />
|-<br />
!align=left |Abstract<br />
||<br />
No abstract in PubMed<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2068975 PubMed]<br />
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!align=left |Keywords<br />
||<br />
Biotransformation; Carcinogens/pharmacokinetics; Cytochrome P-450 Enzyme System/metabolism; Free Radicals; Humans; Oxidation-Reduction<br />
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<references/></div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:2068975&diff=1491288PMID:20689752014-06-23T16:13:08Z<p>54.211.91.134: New PMID: Page!</p>
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'''Jennings, ME, Quick, LN, Soni, A, Davis, RR, Crosby, K, Ott, CM, Nickerson, CA and Wilson, JW''' (2011) Characterization of the Salmonella enterica serovar Typhimurium ydcI gene, which encodes a conserved DNA binding protein required for full acid stress resistance. ''J. Bacteriol.'' '''193''':2208-17<br />
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||<br />
Salmonella enterica serovar Typhimurium possesses a stimulon of genes that are differentially regulated in response to conditions of low fluid shear force that increase bacterial virulence and alter other phenotypes. In this study, we show that a previously uncharacterized member of this stimulon, ydcI or STM1625, encodes a highly conserved DNA binding protein with related homologs present in a range of gram-negative bacterial genera. Gene expression analysis shows that ydcI is expressed in different bacterial genera and is involved in its autoregulation in S. Typhimurium. We demonstrate that purified YdcI protein specifically binds a DNA probe consisting of its own promoter sequence. We constructed an S. Typhimurium ΔydcI mutant strain and show that this strain is more sensitive to both organic and inorganic acid stress than is an isogenic WT strain, and this defect is complemented in trans. Moreover, our data indicate that ydcI is part of the rpoS regulon related to stress resistance. The S. Typhimurium ΔydcI mutant was able to invade cultured cells to the same degree as the WT strain, but a strain in which ydcI expression is induced invaded cells at a level 2.8 times higher than that of the WT. In addition, induction of ydcI expression in S. Typhimurium resulted in the formation of a biofilm in stationary-phase cultures. These data indicate the ydcI gene encodes a conserved DNA binding protein involved with aspects of prokaryotic biology related to stress resistance and possibly virulence.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21398541 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3133089 PMC3133089]<br />
Online version:[http://dx.doi.org/10.1128/JB.01335-10 10.1128/JB.01335-10]<br />
|-<br />
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||<br />
Amino Acid Sequence; Bacterial Proteins/genetics; Bacterial Proteins/metabolism; Biofilms; Conserved Sequence; DNA, Bacterial/metabolism; Gene Expression Regulation, Bacterial/physiology; Molecular Sequence Annotation; Mutation; Salmonella typhimurium/genetics; Salmonella typhimurium/metabolism; Stress, Physiological<br />
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<references/></div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:21398541&diff=1491190PMID:213985412014-06-16T13:22:37Z<p>54.211.91.134: New PMID: Page!</p>
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'''Lelivelt, MJ and Kawula, TH''' (1995) Hsc66, an Hsp70 homolog in Escherichia coli, is induced by cold shock but not by heat shock. ''J. Bacteriol.'' '''177''':4900-7<br />
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!align=left |Abstract<br />
||<br />
Hsc66 is the second identified Hsp70 protein in Escherichia coli. Mutations in hscA, the gene encoding Hsc66, compensate for some phenotypic effects of a mutation in hns, a gene encoding the cold-inducible, nucleoid-associated protein H-NS. Expression of hscA was not induced upon heat shock but was induced approximately 11-fold 3 h after a shift from 37 to 10 degrees C. Furthermore, hscA was induced upon chloramphenicol addition, which induces the synthesis of other cold-inducible genes. Mapping of the transcription initiation site showed that hscA was cotranscribed with an upstream dnaJ-like gene, hscB; thus, hscB was also cold inducible. The hscBA promoter did not contain a Y-box element found in some cold-inducible promoters. Using two-dimensional electrophoresis, we identified Hsc66 under static 37 degrees C growth conditions and showed that Hsc66 was induced, as well as hscA, 3 h after a cold shock. Growth of an hscA mutant following cold shock was monitored relative to that of an isogenic wild-type strain. While cold shock adaptation as a function of growth rate was not significantly impaired in an hscA mutant, the expression of at least five other proteins was altered in this mutant following cold shock. On the basis of the homology to Hsp70 proteins and the induction following cold shock, we speculate that Hsc66 functions as a cold shock molecular chaperone.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7665466 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC177263 PMC177263]<br />
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Bacterial Proteins/biosynthesis; Bacterial Proteins/genetics; Base Sequence; Chloramphenicol/pharmacology; Cold Temperature; Escherichia coli/drug effects; Escherichia coli/genetics; Escherichia coli/growth & development; Escherichia coli Proteins; Gene Expression Regulation, Bacterial; HSP40 Heat-Shock Proteins; HSP70 Heat-Shock Proteins/biosynthesis; HSP70 Heat-Shock Proteins/genetics; Heat-Shock Proteins/biosynthesis; Heat-Shock Proteins/genetics; Hot Temperature; Molecular Chaperones; Molecular Sequence Data; Mutagenesis, Insertional; Promoter Regions, Genetic/genetics; Transcription, Genetic<br />
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<references/></div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:7665466&diff=1491186PMID:76654662014-06-16T11:37:16Z<p>54.211.91.134: New PMID: Page!</p>
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'''Court, R, Cook, N, Saikrishnan, K and Wigley, D''' (2007) The crystal structure of lambda-Gam protein suggests a model for RecBCD inhibition. ''J. Mol. Biol.'' '''371''':25-33<br />
|-<br />
!align=left |Abstract<br />
||<br />
In Escherichia coli, RecBCD processes double-stranded DNA breaks during the initial stages of homologous recombination. RecBCD contains helicase and nuclease activities, and unwinds and digests the blunt-ended DNA until a specific eight-nucleotide sequence, Chi, is encountered. Chi modulates the nuclease activity of RecBCD and results in a resected DNA end, which is a substrate for RecA during subsequent steps in recombination. RecBCD also acts as a defence mechanism against bacteriophage infection by digesting linear viral DNA present during virus replication or resulting from the action of restriction endonucleases. To avoid this fate, bacteriophage lambda encodes the gene Gam whose product is an inhibitor of RecBCD. Gam has been shown to bind to RecBCD and inhibit its helicase and nuclease activities. We show that Gam inhibits RecBCD by preventing it from binding DNA. We have solved the crystal structure of Gam from two different crystal forms. Using the published crystal structure of RecBCD in complex with DNA we suggest models for the molecular mechanism of Gam-mediated inhibition of RecBCD. We also propose that Gam could be a mimetic of single-stranded, and perhaps also double-stranded, DNA.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17544443 PubMed]<br />
Online version:[http://dx.doi.org/10.1016/j.jmb.2007.05.037 10.1016/j.jmb.2007.05.037]<br />
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Bacteriophage lambda/metabolism; Crystallography, X-Ray; DNA/metabolism; DNA-Binding Proteins; Dimerization; Escherichia coli/genetics; Escherichia coli/metabolism; Escherichia coli Proteins/chemistry; Escherichia coli Proteins/genetics; Escherichia coli Proteins/metabolism; Exodeoxyribonuclease V/antagonists & inhibitors; Exodeoxyribonuclease V/chemistry; Exodeoxyribonuclease V/genetics; Exodeoxyribonuclease V/metabolism; Models, Molecular; Molecular Sequence Data; Protein Binding; Protein Conformation; Viral Proteins/chemistry; Viral Proteins/genetics; Viral Proteins/metabolism<br />
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==References==<br />
{{RefHelp}}<br />
<references/></div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:17544443&diff=1491156PMID:175444432014-06-14T07:35:16Z<p>54.211.91.134: New PMID: Page!</p>
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<div>PMID on Demand placeholder</div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:18723630&diff=1491151PMID:187236302014-06-14T03:12:19Z<p>54.211.91.134: Fill PMID: Page!</p>
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'''Jaeger, T and Mayer, C''' (2008) The transcriptional factors MurR and catabolite activator protein regulate N-acetylmuramic acid catabolism in Escherichia coli. ''J. Bacteriol.'' '''190''':6598-608<br />
|-<br />
!align=left |Abstract<br />
||<br />
The MurNAc etherase MurQ of Escherichia coli is essential for the catabolism of the bacterial cell wall sugar N-acetylmuramic acid (MurNAc) obtained either from the environment or from the endogenous cell wall (i.e., recycling). High-level expression of murQ is required for growth on MurNAc as the sole source of carbon and energy, whereas constitutive low-level expression of murQ is sufficient for the recycling of peptidoglycan fragments continuously released from the cell wall during growth of the bacteria. Here we characterize for the first time the expression of murQ and its regulation by MurR, a member of the poorly characterized RpiR/AlsR family of transcriptional regulators. Deleting murR abolished the extensive lag phase observed for E. coli grown on MurNAc and enhanced murQ transcription some 20-fold. MurR forms a stable multimer (most likely a tetramer) and binds to two adjacent inverted repeats within an operator region. In this way MurR represses transcription from the murQ promoter and also interferes with its own transcription. MurNAc-6-phosphate, the substrate of MurQ, was identified as a specific inducer that weakens binding of MurR to the operator. Moreover, murQ transcription depends on the activation by cyclic AMP (cAMP)-catabolite activator protein (CAP) bound to a class I site upstream of the murQ promoter. murR and murQ are divergently orientated and expressed from nonoverlapping face-to-face (convergent) promoters, yielding transcripts that are complementary at their 5' ends. As a consequence of this unusual promoter arrangement, cAMP-CAP also affects murR transcription, presumably by acting as a roadblock for RNA polymerase.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18723630 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2566201 PMC2566201]<br />
Online version:[http://dx.doi.org/10.1128/JB.00642-08 10.1128/JB.00642-08]<br />
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Artificial Gene Fusion; Base Sequence; Cyclic AMP Receptor Protein/metabolism; DNA Footprinting; DNA, Bacterial/metabolism; DNA-Binding Proteins/metabolism; Escherichia coli/physiology; Escherichia coli Proteins/biosynthesis; Escherichia coli Proteins/metabolism; Gene Deletion; Gene Expression Regulation, Bacterial; Gene Order; Genes, Reporter; Glycoside Hydrolases/biosynthesis; Molecular Sequence Data; Muramic Acids/metabolism; Promoter Regions, Genetic; Protein Binding; Transcription Factors/metabolism; beta-Galactosidase/biosynthesis; beta-Galactosidase/genetics<br />
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==References==<br />
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<references/></div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:18723630&diff=1491150PMID:187236302014-06-14T03:12:18Z<p>54.211.91.134: New PMID: Page!</p>
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<div>PMID on Demand placeholder</div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:1905223&diff=1491104PMID:19052232014-06-10T22:12:32Z<p>54.211.91.134: Fill PMID: Page!</p>
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'''Downing, GJ, Yarlagadda, P and Maulik, D''' Effects of acute hypoxemia on umbilical arterial Doppler indices in a fetal ovine model. ''Early Hum. Dev.'' '''25''':1-10<br />
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||<br />
Changes in umbilical arterial Doppler waveform in response to acute maternal hypoxemia were assessed in a chronic ovine model. Maternal heart rate, blood gases, fetal heart rate and umbilical arterial Doppler indices measured at baseline conditions and during periods of maternal hypoxemia were compared. The indices measured were systolic-diastolic ratio (S/D), pulsatility index (PI) and resistance index (RI). Fetal heart rate decreased (less than 80 beats/min) and umbilical arterial Doppler indices increased (P less than 0.001) during the periods of hypoxemia. Furthermore, the Doppler indices were highly but negatively correlated with alterations in the fetal heart rate (FHR) (P less than 0.001). Analysis of the Doppler waveform phase intervals revealed nearly constant systolic intervals while diastolic intervals varied inversely with the heart rate alterations. Moreover, the umbilical arterial Doppler indices, when corrected for FHR changes, were relatively unchanged from baseline measurements. This study indicates that maternal hypoxemia induced changes in the umbilical arterial Doppler indices may be primarily attributable to the changes in FHR.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1905223 PubMed]<br />
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Analysis of Variance; Animals; Anoxia/blood; Blood Pressure; Carbon Dioxide/blood; Female; Fetal Monitoring; Fetus/blood supply; Heart Rate; Heart Rate, Fetal; Hydrogen-Ion Concentration; Oxygen/blood; Pregnancy/blood; Regression Analysis; Sheep; Umbilical Arteries/ultrasonography<br />
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{{LitSignificance}}<br />
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{{LitMaterials}}<br />
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<annotationlinks/><br />
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==References==<br />
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<references/></div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:1905223&diff=1491103PMID:19052232014-06-10T22:12:31Z<p>54.211.91.134: New PMID: Page!</p>
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<div>PMID on Demand placeholder</div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:16751609&diff=1491089PMID:167516092014-06-09T12:28:40Z<p>54.211.91.134: Fill PMID: Page!</p>
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'''Rizk, SS, Cuneo, MJ and Hellinga, HW''' (2006) Identification of cognate ligands for the Escherichia coli phnD protein product and engineering of a reagentless fluorescent biosensor for phosphonates. ''Protein Sci.'' '''15''':1745-51<br />
|-<br />
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||<br />
The Escherichia coli phnD gene is hypothesized to code for the periplasmic binding component of a phosphonate uptake system. Here we report the characterization of the phosphonate-binding properties of the phnD protein product. We find that PhnD exhibits high affinity for 2-aminoethylphosphonate (5 nM), the most commonly occurring natural phosphonate produced by lower eukaryotes, but also binds several other phosphonates with micromolar affinities. A significant number of man-made phosphonates, such as insecticides and chemical warfare agents, are chemical threats and environmental pollutants. Consequently, there is an interest in developing methods for the detection and bioremediation of phosphonates. Bacterial periplasmic-binding proteins have been utilized for developing reagentless biosensors that report analytes by coupling ligand-binding events to changes in the emission properties of a covalently conjugated environmentally-sensitive fluorophore. Several PhnD conjugates described here show large changes in fluorescence upon binding to methylphosphonate (MP), with two conjugates exhibiting up to 50% decrease in emission intensity. Since MP is the final degradation product of many nerve agents, these PhnD conjugates can function as components in a biosensor system for chemical warfare agents.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16751609 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2242554 PMC2242554]<br />
Online version:[http://dx.doi.org/10.1110/ps.062135206 10.1110/ps.062135206]<br />
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||<br />
Biosensing Techniques/methods; Carrier Proteins/chemistry; Carrier Proteins/genetics; Carrier Proteins/metabolism; Chemical Warfare Agents/analysis; Escherichia coli Proteins/chemistry; Escherichia coli Proteins/genetics; Escherichia coli Proteins/metabolism; Fluorescence; Insecticides/analysis; Ligands; Organophosphonates/analysis; Organophosphonates/metabolism; Protein Binding; Protein Engineering<br />
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{{LitSignificance}}<br />
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{{LitMaterials}}<br />
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{{RefHelp}}<br />
<references/></div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:16751609&diff=1491088PMID:167516092014-06-09T12:28:40Z<p>54.211.91.134: New PMID: Page!</p>
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<div>PMID on Demand placeholder</div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:17521287&diff=1491081PMID:175212872014-06-09T02:33:19Z<p>54.211.91.134: Fill PMID: Page!</p>
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'''Clarke, TA, Cole, JA, Richardson, DJ and Hemmings, AM''' (2007) The crystal structure of the pentahaem c-type cytochrome NrfB and characterization of its solution-state interaction with the pentahaem nitrite reductase NrfA. ''Biochem. J.'' '''406''':19-30<br />
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||<br />
NrfB is a small pentahaem electron-transfer protein widely involved in the respiratory reduction of nitrite or nitric oxide to ammonia, processes that provide energy for anaerobic metabolism in many enteric bacteria and also serve to detoxify these reactive nitrogen species. The X-ray crystal structure of Escherichia coli NrfB is presented at 1.74 A (1 A=0.1 nm) resolution. The architecture of the protein is that of a 40 A 'nanowire' in which the five haems are positioned within 6 A of each other along a polypeptide scaffold. During nitrite reduction, the physiological role of NrfB is to mediate electron transfer to another pentahaem protein, NrfA, the enzyme that catalyses periplasmic nitrite or nitric oxide reduction. Protein-protein interaction studies suggest NrfA and NrfB can form a 20-haem NrfA2-NrfB2 heterotetrameric complex.<br />
|-<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17521287 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1948984 PMC1948984]<br />
Online version:[http://dx.doi.org/10.1042/BJ20070321 10.1042/BJ20070321]<br />
|-<br />
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||<br />
Amino Acid Motifs; Amino Acid Sequence; Conserved Sequence; Crystallography, X-Ray; Cytochrome c Group/metabolism; Cytochromes c/chemistry; Cytochromes c/metabolism; Dimerization; Escherichia coli/chemistry; Escherichia coli/enzymology; Escherichia coli Proteins/chemistry; Escherichia coli Proteins/metabolism; Heme/metabolism; Light; Models, Molecular; Molecular Sequence Data; Nitrate Reductases/metabolism; Oxidation-Reduction; Protein Binding; Protein Structure, Tertiary; Scattering, Radiation; Solutions; Spectrometry, Fluorescence; Ultracentrifugation<br />
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{{LitSignificance}}<br />
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{{LitMaterials}}<br />
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==References==<br />
{{RefHelp}}<br />
<references/></div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:17521287&diff=1491080PMID:175212872014-06-09T02:33:19Z<p>54.211.91.134: New PMID: Page!</p>
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<div>PMID on Demand placeholder</div>54.211.91.134https://ecoliwiki.org/colipedia/index.php?title=PMID:17350958&diff=1491050PMID:173509582014-06-07T06:56:39Z<p>54.211.91.134: Fill PMID: Page!</p>
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'''Layer, G, Gaddam, SA, Ayala-Castro, CN, Ollagnier-de Choudens, S, Lascoux, D, Fontecave, M and Outten, FW''' (2007) SufE transfers sulfur from SufS to SufB for iron-sulfur cluster assembly. ''J. Biol. Chem.'' '''282''':13342-50<br />
|-<br />
!align=left |Abstract<br />
||<br />
Iron-sulfur (Fe-S) clusters are key metal cofactors of metabolic, regulatory, and stress response proteins in most organisms. The unique properties of these clusters make them susceptible to disruption by iron starvation or oxidative stress. Both iron and sulfur can be perturbed under stress conditions, leading to Fe-S cluster defects. Bacteria and higher plants contain a specialized system for Fe-S cluster biosynthesis under stress, namely the Suf pathway. In Escherichia coli the Suf pathway consists of six proteins with functions that are only partially characterized. Here we describe how the SufS and SufE proteins interact with the SufBCD protein complex to facilitate sulfur liberation from cysteine and donation for Fe-S cluster assembly. It was previously shown that the cysteine desulfurase SufS donates sulfur to the sulfur transfer protein SufE. We have found here that SufE in turn interacts with the SufB protein for sulfur transfer to that protein. The interaction occurs only if SufC is present. Furthermore, SufB can act as a site for Fe-S cluster assembly in the Suf system. This provides the first evidence of a novel site for Fe-S cluster assembly in the SufBCD complex.<br />
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17350958 PubMed]<br />
Online version:[http://dx.doi.org/10.1074/jbc.M608555200 10.1074/jbc.M608555200]<br />
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||<br />
Biological Transport, Active/physiology; Carrier Proteins/genetics; Carrier Proteins/metabolism; Escherichia coli/genetics; Escherichia coli/metabolism; Escherichia coli Proteins/genetics; Escherichia coli Proteins/metabolism; Iron/metabolism; Lyases/genetics; Lyases/metabolism; Models, Molecular; Multiprotein Complexes/genetics; Multiprotein Complexes/metabolism; Oxidative Stress/physiology; Sulfur/metabolism<br />
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{{LitSignificance}}<br />
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{{LitMaterials}}<br />
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==References==<br />
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<references/></div>54.211.91.134